[gmx-users] floating exceptions
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 11 15:28:00 CET 2002
On Mon, 11 Mar 2002, Lynne E. Bilston wrote:
>I'm having difficulty tracking down why I'm getting floating exceptions
>when I do an energy minimisation prior to doing md.
>I get the same error in both 3.0 and 3.1 for my system (a lipid/protein
>combination), it prints out the energy tolerances, initial energy value,
>and the f-norm, then dies. I think it may be due to anomalies from the
>periodic boundary conditions, as I've just reduced the size of the system
>by trimming some lipids from the edges of a bigger system.
this you can easily test by making the box larger. If you have two atoms
on top of each other you'll get nonsense., Just double the box in all
>I can't figure out how to interpret what I'm getting from the -debug option
>and gmxdump. Is there anywhere I can look to see what all the stuff in
>these files means?
Not really, the debug stuff *was* self explanatory for the person who
wrote the code (at the time of writing). gmxdump should be slightly
more comprehensible, although the topology etc. is quite complex.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users